NCBO Wiki - User contributions [en]

Evolutionary Biology and Ontologies

2017-09-07T16:48:46Z

Hlapp: Fixed URLs to Phenoscape wiki

<center>[[Image:Evolution2008-OntologyWorkshop.png]]</center>

== Introduction ==

This workshop will be held in conjunction with the [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008] meeting in Minneapolis, MN on June 20, 2008. It is organized under the auspices of the [http://ncbo.us National Center for Biomedical Ontologies] (NCBO) in collaboration with the [http://www.nescent.org/ National Evolutionary Synthesis Center] (NESCent).

; [https://wiki.phenoscape.org/wiki/Training_and_Workshops NESCent wiki]

; [https://wiki.phenoscape.org/wg/phenoscape/images/7/71/EBO_Flyer.pdf Workshop flyer]

; [http://www.cce.umn.edu/conferences/evolution/ Venue]

; Organizers: Barry Smith (Buffalo), Paula Mabee (University of South Dakota), Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon)

; Focus: This meeting is focused on the application of ontologies to studies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.

; Goals:
:# Introducing what ontologies are, how they should be built, what makes an ontology useful, and how ontologies help people collaborate across disciplines;
:# Giving illustrations of ontologies actually being used to address problems of interest to evolutionary biologists;
:# Networking and planning: what do we do next in order to advance ontology-based information integration in evolutionary biology?

; Registration: Registration will be open to attendees of the Evolution 2008 conference at no additional cost.

== Agenda ==

*8:00 '''''Registration'''''

*8:30-9:30 '''''Tutorial: An Introduction to Ontology for Evolutionary Biology''''' [https://wiki.phenoscape.org/wg/phenoscape/images/2/22/Smith.ppt Slides]
:Barry Smith, NCBO / Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo

*9:30-10:00 '''''An Introduction to the PATO Phenotype Ontology''''' [https://wiki.phenoscape.org/wg/phenoscape/images/b/b7/Mungall.ppt Slides]
:Chris Mungall, NCBO / University of California, Berkeley
*10:00-10:30 '''''Morning Break'''''

*10:30-11:00 '''''Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases'''''
:Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, OR

*11:00-11:20 '''''An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics'''''
:Paula Mabee, University of South Dakota

*11:20-11:30 '''''Phenote: Curation Software for Evolutionary Phenotypes''''' [https://wiki.phenoscape.org/wg/phenoscape/images/e/ee/Balhoff.pdf Slides]
:James Balhoff, NESCent, Duke University

*11:30-12:00 '''''An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies'''''
:Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, OR

*12:00-1:00 Lunch

*1:00-1:30 '''''Lightning Talks from Workshop Participants'''''

*1:30-2:00 '''''Developing an Ontology for Amphibians using NLP''''' [https://wiki.phenoscape.org/wg/phenoscape/images/1/12/Maglia.ppt Slides]
:Anne Maglia, University of Missouri-Rolla

*2:00-2:30 '''''Ontologies, Image Databases, and Evolutionary Biology''''' [https://wiki.phenoscape.org/wg/phenoscape/images/9/94/Ramirez.pdf Slides]
:Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina

*2:30-2:45 Afternoon Break

*2:45-3:15 '''''An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits''''' [https://wiki.phenoscape.org/wg/phenoscape/images/a/a4/Vision_evont08.pdf Slides]
:Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina

*3:15-3:45 '''''Names, Ranks, Clades, and Taxonomy Ontologies''''' [https://wiki.phenoscape.org/wg/phenoscape/images/5/5b/Midford.ppt Slides]
: Peter Midford, Department of Ecology and Evolutionary Biology, University of Kansas

*3:45-4:00 '''''Synthesis'''''
:Suzanna Lewis, NCBO / University of California, Berkeley and Paula Mabee

== Background Reading ==

[http://obofoundry.org The OBO Foundry]

Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith b. (2008) CARO - The common anatomy reference ontology
http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf
In Anatomy Ontologies for Bioinformatics: Principles and Practice, A. Burger, D. Davidson and R. Baldock (eds).

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) [http://dx.doi.org/10.1016/j.tree.2007.03.013 Phenotype ontologies: the bridge between genomics and evolution]. Trends in Ecology and Evolution 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) [http://psb.stanford.edu/psb-online/proceedings/psb07/maglia.pdf An anatomical ontology for amphibians]. Pacific Symposium on Biocomputing 12: 367-378.

Midford PE (2004) [http://dx.doi.org/10.1093/bioinformatics/bth433 Ontologies for behavior]. Bioinformatics 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) [http://dx.doi/org/10.1080/10635150701313848 Text linking of digital images to phylogenetic data matrices using a morphological ontology]. Systematic Biology 56, 283-94.

Smith B, Ashburner M, Rosse C, et al. [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration], Nature Biotechnology 2007; 25 (11): 1251-1255.

Smith B, Ceusters W, Klagges B, et al., [http://genomebiology.com/2005/6/5/R46 Relations in biomedical ontologies], Genome Biology (2005), 6 (5), R46.

== Additional Resources ==

Michael Bada and Larry Hunter did an analysis of the glossary of terms for the book ''Being Alive'' (by Larry Hunter, forthcoming from MIT Press) found 189 terms that were not mappable to any OBO ontology. About half of these terms were related to evolution or population biology. The [[list of unmatched glossary terms]] is available and may be useful for ensuring the comprehensiveness of an evolutionary biology ontology.

Evolutionary Biology and Ontologies 2009

2009-01-03T23:20:10Z

Hlapp:

This workshop will be held in conjunction with the Annual Meeting of the
Society for Integrative and Comparative Biology ([http://www.sicb.org/meetings/2009/index.php3 SICB]) in Boston, MA on January 5, 2009. It is cosponsored by the National Evolutionary Synthesis Center ([http://www.nescent.org NESCent]) and the National Center for Biomedical Ontologies ([http://bioontology.org NCBO]).

'''Organizers'''
Paula Mabee, Barry Smith, Todd Vision, Monte Westerfield.

'''Goals'''
The workshop is focused on the application of ontologies to studies in comparative biology, with a particular emphasis on morphological and behavioral phenotypes. The goal is to introduce what ontologies are, how they are built, what makes an ontology useful, how ontologies can help researchers collaborate across disciplines, and to highlight several applications of this approach to comparative biology.

'''Registration'''
Registration is open to attendees of the SICB 2009 conference at no additional cost.

'''Agenda'''

January 5, 2009

8:00: Todd Vision (University of North Carolina, NESCent) - Introduction

8:05: Barry Smith (University of Buffalo, NCBO) - An introduction to ontologies for evolutionary biologists

8:35: Monte Westerfield (Zebrafish Information Service, University of
Oregon) - Linking animal models and human diseases

9:00: Paula Mabee (University of South Dakota) - [http://phenoscape.org Phenoscape]: extending model organism ontologies for devo-studies of evolutionary phenotypes

9:20: Wasila Dahdul (University of South Dakota; National Evolutionary
Synthesis Center): The promises and pitfalls of multi-species anatomy
ontologies

9:40: James Balhoff (National Evolutionary Synthesis Center): Software and
database resources for curation and management of evolutionary phenotypes

10:00: BREAK

10:20: Andy Deans (North Carolina State University): Developing a
Hymenopteran ontology

10:50: Peter Midford (University of Kansas): Comparative Analysis of
behavior using ontologies

11:20: Anne Maglia (Missouri University of Science and Technology): Developing an amphibian ontology

11:50: Suzanna Lewis (Berkeley Bioinformatics and Ontology Project): Wrap-up

'''Background Reading'''

Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith B (2008) [http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf CARO - The common anatomy reference ontology] In: Anatomy
''Ontologies for Bioinformatics: Principles and Practice'', A. Burger, D.
Davidson and R. Baldock (eds).

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall
C, Westerfield M (2007) Phenotype ontologies: the bridge between genomics
and evolution. ''Trends in Ecology and Evolution'', 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) An anatomical ontology
for amphibians. ''Pacific Symposium on Biocomputing'', 12: 367-378.

Midford PE (2004) Ontologies for behavior. ''Bioinformatics'', 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) Text linking of digital images to phylogenetic data matrices using a
morphological ontology. ''Systematic Biology'', 56, 283-94.

Smith B, Ashburner M, Rosse C, et al. (2007) [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration]. ''Nature Biotechnology'', 25, 1251-1255.

Smith B, Ceusters W, Klagges B, et al. (2005) [http://genomebiology.com/2005/6/5/R46 Relations in biomedical ontologies]. ''Genome Biology'', 6 (5), R46.

Evolutionary Biology and Ontologies

2008-06-12T16:10:48Z

Hlapp: /* Agenda */

<center>[[Image:Evolution2008-OntologyWorkshop.png]]</center>

== Introduction ==

This workshop will be held in conjunction with the [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008] meeting in Minneapolis, MN on June 20, 2008. It is organized under the auspices of the [http://ncbo.us National Center for Biomedical Ontologies] (NCBO) in collaboration with the [http://www.nescent.org/ National Evolutionary Synthesis Center] (NESCent). Please disseminate widely using the URL for this page, or the [http://www.nescent.org/documents/EBO_Flyer.pdf workshop flyer].

; [http://www.cce.umn.edu/conferences/evolution/ Venue]

; Organizers: Barry Smith (Buffalo), Paula Mabee (University of South Dakota), Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon)

; Focus: This meeting is focused on the application of ontologies to studies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.

; Goals:
:# Introducing what ontologies are, how they should be built, what makes an ontology useful, and how ontologies help people collaborate across disciplines;
:# Giving illustrations of ontologies actually being used to address problems of interest to evolutionary biologists;
:# Networking and planning: what do we do next in order to advance ontology-based information integration in evolutionary biology?

; Registration: Registration will be open to attendees of the Evolution 2008 conference at no additional cost.

== Agenda ==

*8:30-9:30 '''''Tutorial: An Introduction to Ontology for Evolutionary Biology'''''
:Barry Smith, NCBO / Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo

*9:30-10:00 '''''An Introduction to the PATO Phenotype Ontology'''''
:Chris Mungall, NCBO / University of California, Berkeley

*10:00-10:30 '''''Morning Break'''''

*10:30-11:00 '''''Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases'''''
:Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, OR

*11:00-11:30 '''''An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics'''''
:Paula Mabee, University of South Dakota

*11:30-12:00 '''''An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies'''''
:Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, OR

*12:00-1:00 Lunch

*1:00-1:30 '''''Developing an Ontology for Amphibians using NLP'''''
:Anne Maglia, University of Missouri-Rolla

*1:30-2:00 '''''Ontologies, Image Databases, and Evolutionary Biology'''''
:Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina

*2:00-2:30 '''''An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits'''''
:Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina

*2:30-3:00 Afternoon Break

*3:00-3:45 '''''Roundtable & Discussion'''''

*3:45-4:00 '''''Wrap-Up Session: Next Steps'''''
:Suzanna Lewis, NCBO / University of California, Berkeley and Paula Mabee

== Background Reading ==

[http://obofoundry.org The OBO Foundry]

Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith b. (2008) CARO - The common anatomy reference ontology
http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf
In Anatomy Ontologies for Bioinformatics: Principles and Practice, A. Burger, D. Davidson and R. Baldock (eds).

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) [http://dx.doi.org/10.1016/j.tree.2007.03.013 Phenotype ontologies: the bridge between genomics and evolution]. Trends in Ecology and Evolution 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) [http://psb.stanford.edu/psb-online/proceedings/psb07/maglia.pdf An anatomical ontology for amphibians]. Pacific Symposium on Biocomputing 12: 367-378.

Midford PE (2004) [http://dx.doi.org/10.1093/bioinformatics/bth433 Ontologies for behavior]. Bioinformatics 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) [http://dx.doi/org/10.1080/10635150701313848 Text linking of digital images to phylogenetic data matrices using a morphological ontology]. Systematic Biology 56, 283-94.

Smith B, Ashburner M, Rosse C, et al. [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration], Nature Biotechnology 2007; 25 (11): 1251-1255.

== Additional Resources ==

Michael Bada and Larry Hunter did an analysis of the glossary of terms for the book ''Being Alive'' (by Larry Hunter, forthcoming from MIT Press) found 189 terms that were not mappable to any OBO ontology. About half of these terms were related to evolution or population biology. The [[list of unmatched glossary terms]] is available and may be useful for ensuring the comprehensiveness of an evolutionary biology ontology.

Evolutionary Biology and Ontologies

2007-10-18T21:01:48Z

Hlapp:

File:Evolution2008-OntologyWorkshop.png

2007-10-18T20:57:13Z

Hlapp:

Evolutionary Biology and Ontologies

2007-10-18T20:55:59Z

Hlapp: /* Introduction */

== Introduction ==

This workshop will be held in conjunction with the [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008] meeting in Minneapolis, MN, 20 June 2008. It is organized under the auspices of the [http://ncbo.us National Center for Biomedical Ontologies] (NCBO) in collaboration with the [http://www.nescent.org/ National Evolutionary Synthesis Center] (NESCent).

; Organizers: Barry Smith (Buffalo), Paula Mabee (University of South Dakota), Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon)

; Focus: This meeting is focused on the application of ontologies to studies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.

; Goals:
:# Introducing what ontologies are, how they should be built, what makes an ontology useful, and how ontologies help people collaborate across disciplines;
:# Giving illustrations of ontologies actually being used to address problems of interest to evolutionary biologists;
:# Networking and planning: what do we do next in order to advance ontology-based information integration in evolutionary biology?

; Registration: Registration will be open to attendees of the Evolution 2008 conference at no additional cost.

== Draft Agenda ==

*9:00-10.00 Barry Smith, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo; Lead Scientist of the National Center for Biomedical Ontology: Tutorial: An Introduction to Ontology for Evolutionary Biology
*10.00-10.30 Break
*10.30-11.00 Chris Mungall, University of California, Berkeley: An Introduction to the PATO Phenotype Ontology
*11:00-11:30 Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases
*11:30-12:00 Paula Mabee, University of South Dakota: An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics
*12:00 – 1:00 lunch
*1.00-1:45 Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, Oregon: An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies
*1:45-2:15 Anne Maglia, University of Missouri-Rolla: Developing an Ontology for Amphibians using NLP
*2:15 – 2:45 Coffee
*2:45 – 3:15 Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina: Ontologies, Image Databases, and Evolutionary Biology
*3.15—3:45 Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina: An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits
*3:45 – 4:45 Roundtable & Discussion
*4.45-5:00 Suzanna Lewis and Paula Mabee: Wrap-Up Session: Next Steps

== Background Reading ==

[http://obofoundry.org The OBO Foundry]

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) [http://dx.doi.org/10.1016/j.tree.2007.03.013 Phenotype ontologies: the bridge between genomics and evolution]. Trends in Ecology and Evolution 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) [http://psb.stanford.edu/psb-online/proceedings/psb07/maglia.pdf An anatomical ontology for amphibians]. Pacific Symposium on Biocomputing 12: 367-378.

Midford PE (2004) [http://dx.doi.org/10.1093/bioinformatics/bth433 Ontologies for behavior]. Bioinformatics 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) [http://dx.doi/org/10.1080/10635150701313848 Text linking of digital images to phylogenetic data matrices using a morphological ontology]. Systematic Biology 56, 283-94.

Evolutionary Biology and Ontologies

2007-10-18T20:52:05Z

Hlapp:

== Introduction ==

This workshop will be held in conjunction with the [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008] meeting in Minneapolis, MN, 20 June 2008. It is organized under the auspices of the [http://ncbo.us National Center for Biomedical Ontologies] (NCBO) in collaboration with the [http://www.nescent.org/ National Evolutionary Synthesis Center] (NESCent).

'''Organizers'''

Barry Smith (Buffalo), Paula Mabee (University of South Dakota), Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon)

'''Focus'''

This meeting is focused on the application of ontologies to studies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.

'''Goals'''
# Introducing what ontologies are, how they should be built, what makes an ontology useful, and how ontologies help people collaborate across disciplines;
# Giving illustrations of ontologies actually being used to address problems of interest to evolutionary biologists;
# Networking and planning: what do we do next in order to advance ontology-based information integration in evolutionary biology?

'''Registration'''
Registration will be open to attendees of the Evolution 2008 conference at no additional cost.

== Draft Agenda ==

*9:00-10.00 Barry Smith, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo; Lead Scientist of the National Center for Biomedical Ontology: Tutorial: An Introduction to Ontology for Evolutionary Biology
*10.00-10.30 Break
*10.30-11.00 Chris Mungall, University of California, Berkeley: An Introduction to the PATO Phenotype Ontology
*11:00-11:30 Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases
*11:30-12:00 Paula Mabee, University of South Dakota: An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics
*12:00 – 1:00 lunch
*1.00-1:45 Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, Oregon: An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies
*1:45-2:15 Anne Maglia, University of Missouri-Rolla: Developing an Ontology for Amphibians using NLP
*2:15 – 2:45 Coffee
*2:45 – 3:15 Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina: Ontologies, Image Databases, and Evolutionary Biology
*3.15—3:45 Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina: An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits
*3:45 – 4:45 Roundtable & Discussion
*4.45-5:00 Suzanna Lewis and Paula Mabee: Wrap-Up Session: Next Steps

== Background Reading ==

[http://obofoundry.org The OBO Foundry]

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) [http://dx.doi.org/10.1016/j.tree.2007.03.013 Phenotype ontologies: the bridge between genomics and evolution]. Trends in Ecology and Evolution 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) [http://psb.stanford.edu/psb-online/proceedings/psb07/maglia.pdf An anatomical ontology for amphibians]. Pacific Symposium on Biocomputing 12: 367-378.

Midford PE (2004) [http://dx.doi.org/10.1093/bioinformatics/bth433 Ontologies for behavior]. Bioinformatics 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) [http://dx.doi/org/10.1080/10635150701313848 Text linking of digital images to phylogenetic data matrices using a morphological ontology]. Systematic Biology 56, 283-94.

Evolutionary Biology and Ontologies

2007-10-10T19:17:47Z

Hlapp: /* Introduction */

== Introduction ==

This workshop will held in conjunction with the [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008] meeting in Minneapolis, MN, 20 June 2008. It is organized under the auspices of the [http://ncbo.us National Center for Biomedical Ontologies] (NCBO) in collaboration with the [http://www.nescent.org/ National Evolutionary Synthesis Center] (NESCent).

'''Organizers'''

Barry Smith (Buffalo), Paula Mabee (University of South Dakota), Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon)

'''Focus'''

This meeting is focused on the application of ontologies to studies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.

'''Goals'''
# Introducing what ontologies are, how they should be built, what makes an ontology useful, and how ontologies help people collaborate across disciplines;
# Giving illustrations of ontologies actually being used to address problems of interest to evolutionary biologists;
# Networking and planning: what do we do next in order to advance ontology-based information integration in evolutionary biology?

'''Registration'''
Registration will be open to attendees of the Evolution 2008 conference at no additional cost.

== Draft Agenda ==

*9:00-10.00 Barry Smith, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo; Lead Scientist of the National Center for Biomedical Ontology: Tutorial: An Introduction to Ontology for Evolutionary Biology
*10.00-10.30 Break
*10.30-11.00 Chris Mungall, University of California, Berkeley: An Introduction to the PATO Phenotype Ontology
*11:00-11:30 Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases
*11:30-12:00 Paula Mabee, University of South Dakota: An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics
*12:00 – 1:00 lunch
*1.00-1:45 Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, Oregon: An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies
*1:45-2:15 Anne Maglia, University of Missouri-Rolla: Developing an Ontology for Amphibians using NLP
*2:15 – 2:45 Coffee
*2:45 – 3:15 Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina: Ontologies, Image Databases, and Evolutionary Biology
*3.15—3:45 Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina: An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits
*3:45 – 4:45 Roundtable & Discussion
*4.45-5:00 Suzanna Lewis and Paula Mabee: Wrap-Up Session: Next Steps

== Background Reading ==

[http://obofoundry.org The OBO Foundry]

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) [http://dx.doi.org/10.1016/j.tree.2007.03.013 Phenotype ontologies: the bridge between genomics and evolution]. Trends in Ecology and Evolution 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) [http://psb.stanford.edu/psb-online/proceedings/psb07/maglia.pdf An anatomical ontology for amphibians]. Pacific Symposium on Biocomputing 12: 367-378.

Midford PE (2004) [http://dx.doi.org/10.1093/bioinformatics/bth433 Ontologies for behavior]. Bioinformatics 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) [http://dx.doi/org/10.1080/10635150701313848 Text linking of digital images to phylogenetic data matrices using a morphological ontology]. Systematic Biology 56, 283-94.

Evolutionary Biology and Ontologies

2007-10-06T21:34:43Z

Hlapp: /* Draft Agenda */

== Introduction ==

This workshop will held in conjunction with the [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008] meeting in Minnesota, MN, 20 June 2008. It is organized under the auspices of the [http://ncbo.us National Center for Biomedical Ontologies] (NCBO) in collaboration with the [http://www.nescent.org/ National Evolutionary Synthesis Center] (NESCent).

'''Organizers'''

Barry Smith (Buffalo), Paula Mabee (South Dakota), Todd Vision (North Carolina), Monte Westerfield (Oregon)

'''Focus'''

This meeting is focused on the application of ontologies to studies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.

'''Goals'''
*(1) Introducing what ontologies are, how they should be built, what makes an ontology useful, and how ontologies help people collaborate across disciplines;
*(2) Giving illustrations of ontologies actually being used to address problems of interest to evolutionary biologists;
*(3) Networking and planning: what do we do next in order to advance ontology-based information integration in evolutionary biology?

'''Registration'''
Registration will be open to attendees of the Evolution 2008 conference at no additional cost.

== Draft Agenda ==

*9:00-10.00 Barry Smith, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo; Lead Scientist of the National Center for Biomedical Ontology: Tutorial: An Introduction to Ontology for Evolutionary Biology
*10.00-10.30 Break
*10.30-11.00 Chris Mungall, University of California, Berkeley: An Introduction to the PATO Phenotype Ontology
*11:00-11:30 Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases
*11:30-12:00 Paula Mabee, University of South Dakota: An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics
*12:00 – 1:00 lunch
*1.00-1:45 Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, Oregon: An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies
*1:45-2:15 Anne Maglia, University of Missouri-Rolla: Developing an Ontology for Amphibians using NLP
*2:15 – 2:45 Coffee
*2:45 – 3:15 Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina: Ontologies, Image Databases, and Evolutionary Biology
*3.15—3:45 Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina: An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits
*3:45 – 4:45 Roundtable & Discussion
*4.45-5:00 Suzanna Lewis and Paula Mabee: Wrap-Up Session: Next Steps

== Background Reading ==

[http://obofoundry.org The OBO Foundry]

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) [http://dx.doi.org/10.1016/j.tree.2007.03.013 Phenotype ontologies: the bridge between genomics and evolution]. Trends in Ecology and Evolution 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) [http://psb.stanford.edu/psb-online/proceedings/psb07/maglia.pdf An anatomical ontology for amphibians]. Pacific Symposium on Biocomputing 12: 367-378.

Midford PE (2004) [http://dx.doi.org/10.1093/bioinformatics/bth433 Ontologies for behavior]. Bioinformatics 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) [http://dx.doi/org/10.1080/10635150701313848 Text linking of digital images to phylogenetic data matrices using a morphological ontology]. Systematic Biology 56, 283-94.

Phenote:Minutes: June 5, 2007

2007-06-06T14:14:54Z

Hlapp: /* In attendance */

==Talking points==
* joint meeting with NESCent to discuss user interfaces and workflows for their [http://phenomap.nescent.org PhenoMaP] project 8:30-9am.
**see summary of discussion ([[PhenoMaP060507]])
* numbering of configs & versioning
**decided that for NCBO, Nicole would be the 'gatekeeper' of the configuration. Any modifications to the configuration would be discussed/decided within the larger group, then Nicole will update the configuration on the server. The idea will be that major changes would happen on the server, then be distributed via the webstart application. This will probably be the method that zfin will also take as a means to distribute a version to their collaborating labs. We'll set it up so that the user's will always get the most updated version from the webstart.
**Note that this is a pretty good policy for groups to keep in mind. Although this is not the overall policy. Probably needs to be decided within each community.
* display of post composed terms in the table. how do you like the current display? if you don't like it, what might be 'prettier' or better for understanding?
** punted to the obo-phenote mailing list
*solicitation for information about 'expression' configuration. this is a hot topic right now. many groups want to be annotating expression phenotypes. will start discussion on the obo-phenote mailing list, but will set up a obo-phenote-expression list.

==New Phenote features==
05.24.2007, version 1.3 released
* feature: Web-based documentation and Help features [http://www.phenote.org/help check it out here]
* feature: Metadata fields added to configuration. User can name their configuration, add a description, and author
* feature: Descriptions can be added for fields
* feature: Master-to-local overwrite stuff
* feature: Dialog allows user to back out of exiting from File->Exit
* feature: Autocompletion search default settings configurable
* feature: User can save search setting defaults if changed during Phenote session
* feature: Added sample config for BIRN
* feature: Added SAO.obo ontology for BIRN
* feature: Namespace config writes back
* feature: Can specify more than one website for ontology update
* feature: Empty field shows all terms in ontology rather than none
* feature: Can add more differentia to post comp
* change: File->New is disabled until next version
* change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments
* change: can read http, https, ftp, ftps for ontology update URLs, not just http [1718945]
* bugfix: Bulk-editing functions are working again
* bugfix: Undo wasn't working for several functions due to a bug in the Copy function [ 1721044]
* bugfix: multi-select deletes free-text content replaces with * [1721032]
* bugfix: pre 1.2 post comp data wasnt able to load [1721470]
* bugfix: Config update/merge bug where fields in wrong order fixed.

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?
#*want to move the priority of "live reconfigure" higher than the GUI. since it is a necessary part of the GUI configuration spec anyway, will work on this first.
#*want to move up saving changes to 'term history' display preferences

==Q&A==

==Administrative items==
*New: Separating out features from bug requests:
**Please use the "Group" category of "new feature" when submitting a new feature request.

==In attendance==
Mark Gibson, Nicole Washington, Melissa Handell, David Sutherland, Gary Schindelman, Yvonne Bradford, Midori Harris, Michael Ashburner, Hilmar Lapp, Jim Balhoff, Paula Mabee, John Lundberg

Special:Badtitle/NS200:Annotations

2007-05-19T01:14:00Z

Hlapp: /* CToL */

Currently we are not aware of who is using PATO and for what. This is a preliminary list

=Querying OBD=

Alpha version:

* [[OBD:Querying#OBD-Phenotype]]

=Phenotype Annotation FTP Site=

Temporary ftp site:

ftp://ftp.fruitfly.org/pub/obo/obo-phenotype

owl and obo downloads available soon

=Model Organism Phenotype Annotation=

==Paramecium==

ParameciumDB are using PATO for phenotype annotation

==NCBO/ZFIN/FlyBase==

ZFIN and FlyBase are committed to in-depth phenotype annotations as
part of an NCBO Project. As well as residing in each respective MOD's
database, the data will also be collected in a central database called
OBD-Phenotype. This database is being designed around technology such
as OWL in order to make maximum use of the ontologies. We would also
like to populate this database with other OBO-annotated data,
phenotype and otherwise

; http://www.fruitfly.org/~cjm/obd

==Medaka==

MedakaDB are using a subset of PATO for phenotype annotation

=NESCent, CToL, ZFIN collaboration=

The National Evolutionary Synthesis Center ([http://www.nescent.org NESCent]), [http://zfin.org ZFIN], and the [http://bio.slu.edu/mayden/cypriniformes/home.html CToL project] have proposed using PATO for describing phenotypic variation (in particular, morphology) across related species (specifically, among Ostariophysi), and to relate those phenotypic variations to mutant phenotypes observed in Zebrafish, as recorded in the ZFIN database (using PATO, too).

The project is called "[http://phenomap.nescent.org Linking Genomics to Evolution using Phenotype Ontologies]" (or Phenomap in short).

=Mammalian diseases=

MGI are using PATO to coordinate phenotype descriptions that are
associated with diseases (currently OMIM IDs, but soon to be DO IDs)

=BIRN=

=FuGO/OBI=

=Others=

If I have omitted or given short-shrift to anyone please write to the
list and describe your project and/or add it to this page

NCBO News

2006-06-18T18:57:10Z

Hlapp: /* Press Releases */

==Press Releases==
[http://med.stanford.edu/research/spotlight/archive/biocomp_center.html cBiO helps structure data]